User talk:Justin.McCormack/sandbox

Wikipedia Review per section:

Background:

-Lots of good information including quotes from the past and important features of G-quadruplex!

-For the quote used, it probably isn't preferred to say it was "best hypothesized by" because it leads to showing some intonation of being impartial or biased -- I understand what you're getting at by this sentence but Wikipedia might have an issue with this.

-Last sentence of the paragraph is biologically insightful, and could be made more valid if this information was cited (perhaps using your 4th and 5th citation OR use references relating to this information).

- I thought the information in this paragraph flowed very well. Each idea presented eventually lead to the next one.

Cancer

-First paragraph could have a better transition between sentences 3 and 4 -- perhaps the word "However, ... "

-I think sentences 4 and 5 of the first paragraph could be condensed for the purposes of clarity.

-Third paragraph can be rephrased for clarity.

Therapeutics

First paragraph, second sentence seems informationally incomplete. "These complexes have a high affinity for porphyrin rings which makes them effective anticancer agents." -- But what about this binding makes it an effective agent?

First paragraph, third and fourth sentences need grammatical revision.

Ligand Binding

Great information regarding binding pathways. It may be beneficial to the reader to include visuals, such as a pymol image, etc.

Additional Comments

Overall, there was a lot of great information put into this sandbox. It was very well organized, and all of the information seemed to flow well! Great job!!

Maurogarcia21 (talk) 21:01, 13 November 2018 (UTC)

Background
Leg2015 (talk) 22:38, 13 November 2018 (UTC)
 * I'd clarify what you mean by "presence of ideas' in the first sentence. Make sure whatever you put highlights why G-quadruplexes first were studied / were interesting, which I think you were alluding to.
 * Also I'd expand upon the part about the "gel-like substances associated with guanines", maybe talk about why the gel-like substance was an important discovery / how its discovery prompted people's interest in G-quadruplexes. I know you expand upon the findings in the next sentence but commenting on why this discovery was important would help!
 * Would change "the four-stranded DNA structures " to "a four-stranded DNA structure" personally. The grammar's a little squirrely currently
 * I don't know if the quote you mentioned really highlights the importance of G-quadruplexes that much. It would be more intersting to see why finding a four-stranded DNA structure in-vivo is so cool.
 * I would cite the last sentence because you need evidence to back this claim.

Cancer

 * "G-quadruplexes are prevalent in eukaryotic cells especially in telomeres and in 5` unsaturated strands" I think you need a comma between cells and especially
 * "In cancer cells that have mutated helicase these complexes cannot be unwound" need a comma between helicase and these
 * When you saw "these complexes" are you referring to G-quadruplex?
 * You might want to add more about how unwound G-quadruplexes lead to cancerous cells while stabilized G-quadruplex doesn't. I don't understand the difference between unwound and stabilized so that's confusing me a bit.
 * Maybe also highlight a bit more the anticancer properties of G-quadruplex or how it leads to death of cancer cells, because that's an interesting result!
 * Might change "Along with the association of G-quadruplexes in telomeric regions of DNA" to "Along with its prevalence in telomeric..." because that sentence right now is kinda clunky.
 * I'd add a citation to the c-KIT line, there's no such thing as too many citations after all
 * I feel like the first and second paragraph of this section talk about the same process of G-quadruplex stabilization to reduce cell growth. Maybe combine these two pieces into its own paragraph?
 * I'm not sure how your paragraph on c-myc ties into G-quadruplex. I'd be sure to tie in G-quadruplexes more strongly or cut this section out.
 * " With this product" sounds kinda funky as worded

Therapeutics

 * I'd maybe move this section to before the cancer section, because the part about how telomeres are composed of G-quadruplexes helps to inform why telomeres are important to G-quadruplex study in the Cancer section
 * You mention TMPyP4 but never explain what it is.
 * "However TMPyP4 has been limited for used due to its non-selectivity toward cancer cell telomeres and normal double stranded DNA (dsDNA)" needs some rewording, something like: "However TMPyP4 has been limited use as an anticancer agent due to its non-selectivity between cancer cell telomeres and normal double stranded DNA (dsDNA)"
 * "To address this issue analog of TMPyP4 " --> "To address this issue, an analog of TMPyP4 "
 * "Ligand design and development.." sentence is worded a little awkwardly, would revise. Maybe highlight why G-quadruplexes are important to ligand design and development
 * I would highlight more what SYUIQ-05 as a therapeutic is targeting. Is it cancer cell growth? If so, mention that as well
 * "This main pathway of targeting this region results in the lack of telomerase elongation, leading to arrested cell development." --> "The main pathway targeting this region results in lack of telomerase elongation, leading to arrested cell development."
 * "of a single gene target, to minimize unwanted" I'd take out the comma, not necessary

Ligand-Binding

 * This section talks a lot about cancer as well, could maybe be a sub-heading under cancer
 * "MM41, a ligand that ..." I'd add a citation to this line
 * "the best binding is done in parallel with the ligand and quadruplex" I'm not quite sure what this means - I might elaborate more
 * "The side chains and the loops of the quadruplexes are mobile and due to this are able to associate strongly when in the proper conformations" This sentence is also a little confusing as well. I would expand more on why the ligand is able to associate strongly

Overall
This work summarizes some major new points in g-quadruplex breakthroughs. All the right pieces are there, although it could use a bit more of a high level theme or takeaway woven throughout the sections. The content is of good quality, although it does need some grammatical cleaning up and clarification in places. The fluidity could definitely use some work though. As I mentioned before, you've got a lot of really strong pieces, all you need to do now is tie them together! (Easier said than done sometimes though, haha) For formatting, I think you might want to regroup your section structure, unless you'll be placing these points in sections already on the wiki page, in which case ignore this advice. Partner collaboration seemed strong as well. I know I made a lot of comments, but overall it's a really strong piece that just needs some polishing.

Leg2015 (talk) 04:27, 14 November 2018 (UTC)

Other comments: You discuss prevalence of G-quadruplex but I think it is important to indicate how prevalent G-quadruplex forming sequences occur. Are G-quaduruplex structures prevalent or are the G-quadruplex-forming sequence prevalent? There is a difference.

What are 5' unsaturated strands?

Not clear on the role of helicase in cancer cells.

Better explain why G-quad is a target for therapeutics. Why stabilize the structure? How does the therapeutic arrest unregulated cell growth and division? When you list the examples of oncogenes, include c-Myc since you discuss it later.

Can you be more specific on how TmPyP4 interacts with G-quadruplex structures?

Include translocation hotspots also in the beginning where you mention where these sequences are found in the genome.

Is MM41 widely known? Should you compare it to TmPyP4?

the best binding is done in parallel with the ligand and quadruplex-- not clear — Preceding unsigned comment added by DrMZF (talk • contribs) 22:05, 15 November 2018 (UTC)